Some Wounds Run Deep
by JackiLeigh
Summary: Warning: Dark story...violent confrontation between Neal and Peter...and it's aftermath. It's a guilt-ridden, angsty tale with a tissue alert or two thrown in. Thanks for the ideas, everybody.
1. Chapter 1

Some Wounds Run Deep

**AN: WARNING: This story is dark. I like to write dark pieces, on occasion, just to see if I can. And to see if the story can turn out the way I want it to and still be plausible to you readers. I have in mind that Neal attacked El (hence the 'dark' part.) But, first of all, it is TOTALLY out of character. Neal is not a heavy drinker. So he would not get sloppy drunk and do it. And Peter would not have gotten bent out of shape over a hug. He had to perceive his wife was in real danger. **

**So, if you don't mind, help me out here guys. Give me some ideas. I also want to be able to have office angst and trust issues after Neal gets better. Please keep that in mind. I look forward to hearing from you.**

**All that being said, I love a little Neal Whampage and Peter/Neal partner angst. ENJOY this little tasty tidbit. **

Neal had to think fast. He allowed his body to go limp after enduring the repeated blows to his chest and head. He hoped his attacker would see that he was no longer moving, no longer fighting, and stop his assault. It worked. The blows and kicks stopped.

"Neal?!" Peter stopped, looking down at the bloody face that belonged to his C.I. and his friend. Stunned by what he had done, he pulled a now unconscious Caffrey into his arms. Neal had passed out seconds earlier. His head fell back against Peter's arm and his left arm hung limply from its socket.

Neal had been attacked in the Burke's small hallway behind the bookcase. He had blood oozing from his mouth and his nose. His ribs and nose were broken. He had a concussion, and he was bleeding internally.

Peter ignored the blood and moved his fingers to the correct spot on Neal's neck, checking for a pulse. It was weak, but it was there.

Peter was now also aware of his wife's voice. "He didn't' hurt me, Peter! He…he didn't' hurt me! I…." She moved her hands to touch Neal's face, as tears streamed down hers. She had never seen Peter so angry before. She had, only moments before, been screaming for Peter to stop.

Peter's assault on Neal had been short, but it had been brutal. He looked at his wife, a mixture of horror at the realization of what he had done and a deep, deep regret blended on his face.

El somehow managed to stand and went into the kitchen. She called the police. She then grabbed a dish towel and wet it, hoping to clean some of the blood from Neal's face. She was almost finished by the time the paramedics arrived.

The man and women team had to cajole Peter. He was not ready to give Neal over to them. He didn't to let go of his friend. He had been sitting, ever since he had realized what he had done, his back against the wall whispering apologies. There were tears streaming down his face when he looked up at the paramedics and agreed to let Neal go.

Peter stood up slowly, using the wall for support. His legs suddenly felt weak, and the female paramedic asked Peter to come along to be check out. Peter shook his head. He looked down at his shirt. It had a great deal of blood on it. But, he know, none of it was his. Peter looked at his bruised and bleeding knuckles also.

It was like he was waking up from a nightmare. Who was this guy who had attacked Neal?

TBC

**END NOTES: Again, I thank you for your ideas. This is as far as I get. I just cannot see Neal and El in a 'rape scenario.' Plus, I just don't write those type stories. But that, right now, that seems to be the only thing that is plausible. I…I really, really need you guys' help. If I can't find a suitable reason…I'll just pull the story. Thanks again, Jackie.**


	2. Chapter 2

Chapter 2

**AN: Thanks to ****RyomaEchizenChan,**** I like your idea. **

El took over as soon as the paramedics got Neal out of the house. Peter was still leaning against the wall, staring at his hands.

"Hon." El said, gently, to her husband. "Hon." She repeated.

Peter looked up at her than down at his hands. "I…I did that to him."

El didn't reply. She just encouraged her husband to move. Soon they were out the door and on the way to the hospital.

Peter spent the short trip to the hospital staring out the window lost in his thoughts. He knew he had misjudged the scene in his living room. He knew Neal. He had memorized Neal's file before he was caught, for goodness sake. Peter KNEW the man. And Neal was not a violent person. Neal had proved that over and over as his CI, preferring to talk his way out a jam. Peter didn't know if he should scream because of his own stupidity and misdirected anger, or cry because of the pain and injury he had inflicted on his friend.

El kept an eye on her husband as she drove. She wanted to tell him everything. She needed to tell him everything. But right now just was not a good time. Peter was in no condition to receive or understand any of it.

Peter was taken into of the ER treatment rooms also by one of the nurses when she noticed the blood on his shirt and the condition of his hands. He was given a quick exam, the blood cleaned from his hands, and released. He joined his wife in the waiting room about 45 minutes later.

"Any word? Anything?" Peter asked as he sat down beside his wife.

El shook her head. "I called June. She's on her way. I debated calling Reese, but I know one of the first things he'll ask is how Neal is. And we just don't know that yet."

Peter nodded. He had had time to calm down a little. "I screwed up El. I screwed up so damned bad. And Neal is going to have to pay for it, even more than he already has. He'll go back to jail."

El looked at him. "Why?"

"I petitioned for this CI thing. Nobody else it the department really wanted to do it. They all thought it was a bad idea. I had to talk Reese into it." Peter paused. "And now, despite all the cases we've solved. Despite my showing that the relationship can work, nobody else will take him on. Nobody else will want to partner with Neal."

El opened her mouth to speak.

Peter knew what she as going to ask. "Two reasons, first of all, Neal would never be reassigned to me. Second of all, Neal would never WANT to be reassigned to me."

"I think you underestimate Neal."

"It's not about underestimating anybody, El. Neal will never trust me again." Peter stood and started to pace. "And I wouldn't blame him. I don't deserve his trust."

Peter paced for a few more moments. He then sat down and buried his head in his hands.

TBC


	3. Chapter 3

Chapter 3

**AN: Thanks again for favoriting and following me. I am getting to the 'good stuff,' I promise. I just needed to lay a little background and explain a few things. I will try to make this chapter a little longer, but no guarantees. Also, thanks for pointing out things I didn't even think about, like the police or the 'battery' issue (Thanks ****leonore09****). I appreciate that you guys are keeping me on my toes. Sorry I haven't been able to communicate with you all, or post. My service has been down for the past few days. Thanks for your patience.**

A police cruiser had followed Peter and El to the hospital. They had given Peter a lot more leeway than he deserved. The officer stepped up and spoke.

"Agent Burke, we need to go. We did you a favor by not taking you on in and letting you come to the hospital. But it's time you came with us." The officer stated.

Peter nodded. He would have and wanted to protest to stay longer. But the officer was right. They had done him a HUGE favor. He had given them a few details. But in his own mind, he was still reeling from what had happened. The police only had to look at Peter, to see the blood on his hands and shirt, to see he was involved in the attack.

It was all catching up with her, El took a deep breath. She had managed to appear calm, she was not sure how. On the inside she was not sure if she should laugh at the absurdity of what had happened or cry at the reality. She felt herself wiping away tears. Then she realized she was shaking. She collapsed into her husband's arms, crying.

Peter could only hold his wife for a few seconds before it was time to go.

El watched her husband walk away, escorted by two members of the NYPD.

June had been at the hospital only a few minutes, and she still knew nothing about how or why Neal had ended up there. She also knew the people who had all the answers were in no shape to supply them to her at this time. She had seen Peter being led away by the police, and that only added to her confusion and her need to know.

June was about to ask El what had happened when Neal's doctor appeared.

"We are about to take Mr. Caffrey up to surgery. His blood pressure is good. But he is still unconscious, that is a cause for concern. He has a concussion. His ribs are also broken, as is his nose. We are going in because we suspect internal bleeding." The doctor stated.

Both women were speechless. They had no idea of the extent of Neal's injuries. Both women nodded, tears in their eyes.

El then called Reese Hughes. He wanted Reese to find out the truth from her and not through the FBI grapevine. She told her tale as June listened to El's side of the conversation.

***Flashback***

El had opened her door to a panicked Neal. Neal rushed inside. El could never ever remember seeing him like this.

"You need to get out of the house immediately! We need to go!" Neal kept looking back over his shoulder, as if someone was right on his heels.

El went to grab a jacket and her purse, it was close by.

"We need to go! Now El! Come on!" Neal stated

But El had protested, first of all, she had wanted to know what was wrong, what was going on. Second of all, she wanted to wait for Peter.

Neal took her by the arm, with a little more force than he had intended. He was dragging, pulling her towards the back door. He needed to get them out the back and through the ally to where Mozzie was waiting.

Neal heard the front door rattling. He had no idea it was Peter home for lunch. He just kicked into overdrive. He pulled harder to get El to the back door and safety.

"Peter!" El called to him, fear and confusion in her eyes.

"What the…?!" Peter's eyes locked on his wife's as she called out to him. Peter then went into protector mode. He dropped his jacket and briefcase as the memories of coming home to the scene right after Keller had kidnapped El came to his mind. He launched himself at the perpetrator. Peter slammed Neal's head against the wall in the Burke family hall.

Neal crumbled to the floor immediately, stunned, as Peter continued his assault. Neal tried to fight back. But he could not talk or breath very well and soon passed out. It was only El repeatedly screaming for him to stop that got Peter's attention. Peter then looked down at what he had done, who he had attacked.

***End Flashback***

El finished telling her tale just as a nurse came out to give them an update. The nurse said she expected the surgery to last for another hour and then Neal's surgeon would be out to speak with them then.

El gave Reese the update from the nurse. She then told him that Neal had mentioned something about Mozzie and street contacts. Neal kept telling her she was in danger and that they needed to leave. She hung up the phone with Reese.

El then left June to look after Neal, and she went to the police station.

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Peter finished his statement just as El walked in. Peter stood up and greeted his wife, drawing her into his arms.

"How is he?" Peter asked. "What happened? Why was Neal there?"

"He's hurt, Peter." El replied. "That's how he is." El replied, her tears overwhelming her again. "How could you…?" She couldn't even finish she was so upset with him.

Peter could feel his wife's anger, and he knew it was directed at him. He just shook his head and held her.

It took El a moment to calm down again. "What are they going to do?"

Peter sighed. "They said, since I am a federal agent. And ONLY because I'm a federal agent, they are going to let me stay free, on bond, until trial. And depending on Neal's…."

"Neal has a broken nose, broken ribs, a concussion and internal bleeding. And the doctor didn't like it that he had not woken up yet." El said. She was still angry, and she wanted her husband to know just how much damage he had caused.

"El, I…." Peter started shaking his head. He couldn't believe the amount of injury he had inflicted on Neal. "Him not waking up…that's…."

"He came to the house to get me out." El explained. "Neal seemed to think that I was in immediate danger. He was pushing me towards the back door when you came in. He…."

Peter shook his head. "I had flashbacks of Keller. I didn't even recognize him as being Neal. I…I just reacted. I would never have hurt Neal, El. You have to believe me." Peter pleaded. "If I had realized, had known, it was him…." Peter shook his head again. He was really feeling the pain and regret of his actions.

El nodded. She was still angry, but, at least, she was beginning to understand.

TBC

**END NOTES: If I have missed something, or if it still doesn't seem realistic to you, let me know. I realize that some of you may have a problem with Peter being let go, on bail, for such a violent attack. But I do know that agencies help one another out. And I think, if they looked at Peter's record, which is probably procedure. They would have seen that it was just an isolated incident. And he was trying to protect his wife, after all. So I think that that worked in his favor.**


	4. Chapter 4

Some Wounds Run Deep

Chapter 4

**AN: Again, this chapter may be a little OOC for some of you. But I can see Peter having the reaction he had. Sure, he's seen bad things on the job. But he could use his 'professional detachment.' He didn't know those people. He knows Neal.**

June was allowed into Neal's room after his surgery. She had had to 'remind' them who had donated a wing to the hospital. But it was well worth it, even if the sight in front of her troubled her greatly.

The active, young man she knew was lost in bruises and machines. Huge angry black and purple bruises stood out on his face and chest under stark white bandages. And his small, lean frame was made to look even smaller by the number of machines around his bed. He looked lost in a mass of tubes and wires.

June reached through the mass and brushed a soft black curl off Neal's forehead. She then leaned down and lightly kissed his uninjured cheek. "You are going to be alright, Darlin'. We just need you to wake up." June whispered in his ear. "Please be alright." She muttered as she pulled a chair up beside Neal's bed and sat down. She then snaked her hand, again, through the wires and tubes to hold his.

June could not believe the story El hold told Reese. She had trouble seeing Peter hurt Neal. She had trouble seeing him attacking Neal. And she knew, in her heart, Neal would never had hurt El. He's just not a violent man. Neal would prefer to charm and talk his way out of trouble. She sighed, shook her head, and looked at the young man she had come to care a great deal about.

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El's anger flared anew at her husband when she entered Neal's hospital room. It hurt, deeply, to see someone she cared so much about, someone she considered a friend, hurt so badly.

El didn't have to tell Peter how she felt. All he had to do was to look at her face. Peter looked at Neal. He saw the bruises and tubes. But mostly, he saw the ventilator. The idea of the machine terrified him. To actually see it in use, on Neal, Peter backed himself up against the wall. He felt as if he would throw up. Then he felt as if the air in the room has just gone stale. He made a beeline for the door. He stopped just outside in the hall. He took a deep breath, and waited for the feeling of nausea to pass.

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A couple of days later Neal opened his eyes, immediately regretting the action. He still had the mild lingering throb of a headache. And now the bright light of day was assaulting his eyes. He groaned and turned his head. The two women in the room were immediately on their feet. Elizabeth saw Neal turn his head away from the light and quickly pulled the shades. June slipped her hand into his and talked to him. She hit the button for the nurse.

Neal was surprised to see El. The last he remembered…well, he didn't remember a lot. His head was still hurting. He closed his eyes again, and opened them, sure he was hallucinating.

"Elizabeth?" Neal asked, unsure of himself.

El nodded and took his hand. "I'm here, Sweetie."

"El?" Neal was still unsure. He didn't know why he would be in a hospital either. But he would save those questions for later.

Elizabeth took his hand and put it to her face. "I'm right here. I'm okay."

The nurse chose that moment to walk in. She ushered both women out the door. Elizabeth took that time to update everybody on Neal's status.

El and June were allowed back in twenty minutes later. Neal looked a lot more alert. El knew his headache wasn't gone. Even the overhead lights were hurting his eyes. But she had needed to know one thing.

"Neal, honey, I told Pe…." El was about to say 'Peter' but she was not sure if that was a subject to be talking about right now. "The FBI has me under protection ever since I told them what you said. They aren't taking any chances. There is an agent standing guard outside this room right now." El paused. "But, Neal, you never said who was after me." El stated. She hoped she wasn't pushing things, and the thought of someone being after her or Peter terrified her. Besides all that, Neal had just woken up.

"The dog bite…." Neal replied.

El looked at Neal. "What?"

"Satch." Neal said.

El thought for a moment. "The guy Satch bit?"

Neal nodded.

"That was the guy?"

Neal nodded, again.

"You're sure?"

He nodded a third time. Neal fell asleep as Elizabeth exited the room to tell Diana and Jones the latest.

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The man Neal named was picked up in less than 48 hours. The man had talked to several people. But they had backed out when they found out who the target was. No one wanted the FBI on their ass. He finally found two guys willing to do the job for him for a couple grand each. It appeared his pride had been wounded when Elizabeth had fooled him into thinking his wound was infected. And then her escaping had only added insult to injury. He had wanted to get a little revenge. They could not charge him, since no crime was committed. They scared him so badly he started confessing to other crimes he committed, crimes that did earn him some actual jail time.

Peter paced the floor back at his home. Two days had passed since Neal had woken up. He had told El to go on to the hospital after she had left the police station. And she had been going regularly since. The agents assigned to her protection detail following her. They then took turns standing outside the door to Neal's room and following everywhere else she went. The detail was called off when the man was finally jailed.

Peter was thrilled that Neal was awake. He was happy that Neal was able to tell her exactly who was after her. And he had wanted to get into the car about a million times and drive himself to the hospital, but he was afraid. Peter didn't want to upset Neal, if Neal remembered. And Peter didn't want to see that look of fear, possibly hatred, in Neal's eyes if he did.

Peter made up his mind. He grabbed his coat and left the house. He had to know where he stood with Neal.

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Peter stopped just outside Neal's door. He had had a discussion with Neal's doctor. And Peter had given the doctor the short version of what had happened. The doctor initially suggested that Peter delay his visit by a couple more days, until Neal was stronger. But he could tell Peter was anxious to talk to the young man. The doctor gave his permission, but only if Neal agreed to see him.

The doctor spoke to Neal and Neal agreed to see Peter. But Peter could never have anticipated the reception he would receive.

"Hi, Neal." Peter said, unsure of himself as he stepped into the room.

"Why don't you trust me?" Neal demanded.

"Neal, I…." Peter was a little shocked by Neal's question.

"You really think I would hurt Elizabeth!" Neal stated. "Really?"

"Neal…I didn't know it was…I just reacted." Peter explained.

"Get Out!" Neal hissed.

Peter stood, staring.

"Get…Out!" Neal said, raising his voice.

Peter turned and left. He had his answer.

El was astounded. She had no idea how Neal was going to react, what he was going to say. But she had not expected that. She cast a glance back at Neal before walking out the door.

Peter sighed and looked at his wife when they got to the small waiting room at the end of the hall.

"He's angry, I know…but he…." El said. She understood Neal's anger, but this WAS her husband.

Peter shook his head, stopping her. "He's right. He has every right to be angry. I know he wouldn't hurt you. I know that. And I…I can't ask him to trust me. I can't expect him to." He then started to turn and walk away.

"Hon." El pleaded.

"I could have killed him, El. I could have killed him." Peter said, his voice shaking. "I don't know what would have happened if I had. I don't know what I would have done."

El didn't know what to say. She had never seen Peter look so tortured, or so lost. She said goodbye to Neal and followed Peter home.

TBC

**END NOTE: I thank you all, again, for following this story. I'm glad it's not too OOC you can't enjoy it. But I do have a problem. I have not addressed the question of jail time for Peter because I am not sure if he would lose his job if he were to be jailed. I know Neal, for example, cannot be an FBI agent because of his conviction. Does it matter if it's a misdemeanor versus a felony offense? If Peter is convicted of his assault on Neal, could he lose his job? I know, I may be over-thinking this. But since it is so OOC in some respects, I want it to be as right as possible in others. I looked online, but can't find the answers to my questions. If Peter would lose his job, I have another issue I have to come up with an answer to.**


	5. Chapter 5

Chapter 5

Peter had been suspended for 6 months without pay for gross misconduct. And he still had the trial for assault and battery on Neal coming up. He spent his days watching ESPN and his nights lying awake, staring at the ceiling. His mind was too full, too active, to allow his body to rest.

"Hon, you need to rest. Try to sleep." El said when she woke up at 3 a.m. to her husband reading, in bed, beside her.

Peter just shook his head.

"Did you try the sleeping pills the doctor gave you?" El asked.

"I can't take those things. I feel like a zombie the next day." Peter replied.

"Then we go back to the doctor and, he'll give you some you can take." El reasoned.

"You know how much I hate taking pills."

"And you know how much I hate to see you suffer when there is no reason for it." El sat up in bed a little more.

"There's plenty of reason."

El sighed and shook her head. "It's been a couple weeks, Neal's home. They released him yesterday. Go talk to him."

"If it went like it did last time…." Peter shook his head.

"It won't." El reassured him.

Peter looked at her. "What do you know? What did he say?" El had still been going to see Neal on a regular basis.

"He doesn't hate you." El said.

Peter looked at her, again. "How do you know?"

"He doesn't hate you." El repeated.

"He doesn't trust me, El. In a lot of ways, that's much, much worse." Peter replied.

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Three days later El walked in on quite a scene. She couldn't help but smile. Neal was sitting up in bed having his pillow fluffed. He was being pampered to within an inch of his life. He looked at El, and pleaded with her, silently, for help.

"Hey, Neal." El said, making her presence known. She then acknowledged the members of June's staff, present. "If Neal needs anything, I'll let you know."

The staff nodded and left.

"Thank you." Neal said, getting out of bed. He had on a T-shirt and a pair of Pajama pants. He was still a little sore. But he was able to get up and, at least, go to the bathroom on his own. "June is so afraid something is going to happen to me up here and nobody will hear me. Nobody will know I'm hurt. She's been smothering me with all the attention." Neal explained. "I'm not used to it. And I don't know how to tell her that I just don't need it." Neal sighed. "I love that she's concerned…."

El went over to him and hugged him, gently, mindful of his ribs. "Let her spoil you, Neal. She…she really has a soft spot for you. Let her do this…all her kids are grown. She doesn't get to see her grandchildren that often…."

Neal nodded. He knew where she was going with this. "I'll give her another day or two. That's it."

El nodded. "Good."

"I never did thank you." Neal replied.

"For what?"

"For staying with me in the hospital, I know that sometimes you brought your work with you so you could stay and sit with me. I…I just want you to know how much I appreciate that." Neal stated.

"Peter and I care deeply for you."

Neal's mood changed at the mention of Peter's name. "Let's leave your husband out of this."

"Peter…." El started, wanting to tell Neal what Peter had been going through.

"Peter put me in the hospital." Neal replied. He voice cold. "He broke my ribs and busted my nose."

"Neal, he…." El tried again.

"You didn't have to see him, El." Neal said. "You didn't have to look him in the eye and realize he didn't recognize you. You weren't the one lying there, wondering if you were going to die."

El shook her head, tears on her cheeks. "I had no idea. I didn't know. Peter…he didn't…. He didn't tell me anything. He's just…he's hurting, Neal. He feels so guilty…."

Neal just looked at her and then turned away.

"He's not sleeping, Neal." El explained. "He's been to doctors. They have diagnosed him with depression. They think…."

Neal looked at her and shook his head. "I'm not feeling bad for him, El." Neal paused. "You didn't have to look into the face of somebody you trusted and wonder if he was going to kill you."

"I'm sorry, Neal." El said, hugging him again. "I am so sorry."

Neal hugged her back and sighed. "Me too."

TBC


	6. Chapter 6

Chapter 6

**AN: Thanks to you all for following, favoriting, and reviewing. I plan on making this my last chapter. The journey with this story has been most interesting. Thanks, again, to those of you who came along for the ride.**

Peter slipped up the stairs. He didn't have to knock, the door was open. He stood in the doorway, just watching Neal. He had never watched Neal paint before. He looked on amazed as Neal turned the blank canvas into a work of art.

"You stand there any longer, like that, and somebody is going to mistake you for a coat rack." Neal said, finishing up with the last touch ups.

Peter smiled. Of course Neal knew he was standing there.

Peter stepped into the room. "I just wanted to know…why?"

Neal stopped painting and looked at him. "You WANTED to go to jail?"

"No, but…."

"Six months suspension and a load of psych evals aren't enough for you?" Neal asked.

"How did you?" El could have told Neal about the suspension, easy enough. But the amount and depth of the psych evals, he had not discussed that with her. Peter stared at him.

"Hughes has decided to make me his pet-convict for a while." Neal explained. He involuntarily shivered. "He's been telling me all that has gone on with you. He's talked with me, quite a bit, about why I didn't press charges. He wanted to understand what was going on, my reasoning."

Peter smiled at Neal's reaction. "Believe it, or not, Hughes likes you. He wants to keep you around."

Both men were silent for a few moments.

"What was your reasoning? Why…?" Peter asked.

Neal looked at him for a second. "The man I saw that afternoon. The man who came after me was not you. I don't know how to explain it. But…it was just liked somebody else pushed you out and stepped in. When I looked you in the eyes I could tell it wasn't you." He shook his head. "I know it doesn't make sense."

"I get it." Peter replied.

"This is…it's gonna take time."

Peter nodded. He understood completely. "I'm willing to do, whatever it takes, for you to trust me again." Peter replied.

There was another moment of silence.

"You know, I've never told you how talented an artist I think you are." Peter stated.

"Thank you, Peter."

"Thank you, Neal." Peter replied, his statement full of underlying meaning.

THE END


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